I haven’t used 10.5 or 11 yet, so maybe this has already been remedied
But I’ve noticed with Control Room, specifically, control room inserts - if you have an improper shutdown or crash, you will lose settings/plugins that were added or removed since initial program launch.
Pretty certain this happens regardless of whether you’ve saved the project or not, as Control Room inserts are a global entity.
+1
The way saving is done in Cubase is horrible. Unless you exit Cubase safely just after making the adjustments in different places in Cubase, all changes are lost when a crash happens. Why does the user have to think strategically and anticipate losing data on crash when making simple things like changing key commands? Shouldn’t it be sorted out by the developer?
I think any changes made within Cubase settings should be saved just after making them, not when the application closes - which btw hangs upon closing 90% of time - since forever. As a result, the adjustments are lost.
yes I agree, this should almost be a separate feature request but It has mostly been an issue with the control room.
Another really annoying instance it happened, was with the order of my Direct Offline Processing favourite, I had them all in a certain order across the array of offered favourites pages and had a crash, and it reset the order. 
I agrree. But, if I had to guess. It’s designed this way to prevent settings that would crash Cubase from persisting. We do have safe mode these days, however, so I agree that they should take a look at this and see if they can improve it.